4YPL

Crystal structure of a hexameric LonA protease bound to three ADPs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insights into the Allosteric Operation of the Lon AAA+ Protease

Lin, C.-C.Su, S.-C.Su, M.-Y.Liang, P.-H.Feng, C.-C.Wu, S.-H.Chang, C.-I.

(2016) Structure 24: 667-675

  • DOI: 10.1016/j.str.2016.03.001
  • Primary Citation of Related Structures:  
    4YPL, 4YPN

  • PubMed Abstract: 
  • The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by subs ...

    The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC. Electronic address: chungi@gate.sinica.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lon proteaseA, B, C, D, E, F555Meiothermus taiwanensisMutation(s): 1 
Gene Names: lonA1lon
EC: 3.4.21.53
Find proteins for A0A059VAZ3 (Meiothermus taiwanensis)
Explore A0A059VAZ3 
Go to UniProtKB:  A0A059VAZ3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
B, D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
4KZ
Query on 4KZ

Download CCD File 
A, B, C, D, E, F
N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide
C22 H23 B N4 O4
ILENEQWIGPQYCQ-ICSRJNTNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/319 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.044α = 90
b = 169.128β = 90
c = 135.361γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations